RP2 p.Ser99=
c.297C>T · rs782310446 · VCV2808699
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00865%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.5 | GERP -3.6 |
| Overall | ||
| CADD | 2.332 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00865%
African / African-American · 5/57,791 alleles
Filtering AF
0.00336%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00213%
Overall
0.000578%
7/1,211,616 alleles · very rare
exomes 7/1,098,084 · genomes 0/113,532 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00865% | 11,558 |
| Admixed American | 0.00218% | 45,973 |
| European (non-Finnish) | 0.000112% | 895,399 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- RP2
- Protein
- p.Ser99=
- Coding
- c.297C>T
- MANE Select
- NM_006915
- dbSNP
- rs782310446
- Type
- single nucleotide variant
- Location
- chrX:46853670 (GRCh38)
- Structure
- AlphaFold pLDDT 91.64 · 3 PDB
- Residue 99
- the c-cap/cofactor c-like domain; a β-strand; a binding site
Similar variants
- RP2 p.Ser99Arg Uncertain significance ★ ⚠ same residue
- RP2 p.Ser99fs Likely pathogenic ★ same residue
- RP2 c.768+1G>T Pathogenic ★★ same type
- RP2 c.884-1G>A Pathogenic ★★ same type
- RP2 c.969+2T>C Pathogenic/Likely pathogenic ★★ same type
- RP2 c.969+3A>G Pathogenic ★★ same type
- RP2 p.Arg118Cys Pathogenic/Likely pathogenic ★★ same type
- RP2 p.Arg118His Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/rp2-p-ser99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown